R markdown document.---
title: "rmarkdown_pdf"
author: "Sébastien Renaut"
date: '2018-09-06'
output:
html_document:
toc: yes
theme: cerulean
---
---
title: "rmarkdown_docx"
author: "Sébastien Renaut"
date: '2018-09-06'
output:
word_document:
toc: yes
---
You can specify it when you create a new Rmarkdown document.
You can also specify it later in the header.
Then, it’s just a matter of kniting the document!
Little documentation, few options & configurations are possible (This is probably not the format that should be promoted, as it moves away from an open source environment).
Can specify a LibreOffice OpenDocument Text (output: odt_document) or Rich Text Format (output: rtf_document) instead
FYI, there is a spellchecker in Rstudio: Edit >Check Spelling…
---
title: "rmarkdown_pdf"
author: "Sébastien Renaut"
date: '2018-09-06'
output:
pdf_document:
keep_tex: true
toc: yes
---
R markdown pdf_document function in R.LaTeX software is a high-quality typesetting system.
It is the de facto standard for the communication and publication of scientific documents.
LaTeX is available as free software here.
If interested, follow this discussion: Why LaTeX is such a bloated system?
So…TinyTeX is a custom LaTeX distribution that is small in size (~150MB) but functions well in most cases, especially for
R users .
tinytex R package is a wrapper function that installs TinyTeX.
tinytex R package from the console and run install_tinytex(). It may take a few minutes to download and compile (~150MB).install.packages("tinytex")
library(tinytex)
install_tinytex()
Now compile it as a Word document (.docx)
Add some reference by specifying the csl: ../csl/peerj.csl and bibliography: ../biblio/test_library.bib in the header
This allows further options in the .Rmd file when going from .tex file to .pdf.
You can build your own .tex template if you know LaTeX…
There are many templates available on the web that you can use.
Here is one I like for manuscripts (Thanks svmiller on )
Let’s briefly examine and knit the svm-rmarkdown-cv.Rmd file in the reference_material directory.
You should know have all the tools to generate your fully reproducible manuscripts in R.
The only real objection I see in formatting manuscript this way is integrating comments from co-authors who do not use R, R markdown, git or github.
R packages rticles is (potentially) a nice package to format articles according to the specification of a journal.
But first, you need to install it in the R console.
Once installed, try starting a new R markdown document according to your journal of interest.
Right now, few templates available.
Some templates may be slower to render (e.g PNAS), depending on what LaTeX package they depend on and need to be downloaded.
---
title: "Untitled"
author: "Sebastien Renaut"
date: "27/02/2019"
output: ioslides_presentation
---
Remember this:
You can generate your .tex file, upload it to a github repo and Overleaf will connect to it. Others can then collaborate and modify the .tex file via overleaf platform.
Let’s take a quick look at overleaf. Once you have an overleaf account, you can connect it to a github repository and .tex document. You can then pull/push from overleaf to github, allowing others to modify your .tex file.
How do I connect an Overleaf project with a repo on GitHub, GitLab or BitBucket?